In this section we will take raw microbiome count data and turn it
into a clean, analysis-ready phyloseq object. You will:
refs_tree.treefile)
microbiome_references
tutorial.refs_aligned_mafft.fasta)
microbiome_references
tutorial.tax_table.RData)
microbiome_alignments
tutorial.sample_table.RData)
metadata_setup
tutorial and then prepared for microbiomes in
[microbiome_alignments]((https://rich-molecular-health-lab.github.io/tutorials/microbiome_alignments.html).otu_table.RData)
microbiome_alignments
tutorial.phyloseq_genus.RData)phyloseq_melt_genus.RData) for
ggplot workflowstree_genus.RData)In this script we mostly use the phyloseq package,
designed for microbiome analysis.
phyloseq UtilityNote: there is much overlap between
phyloseq,microeco, andmicrobiome, but each makes some steps more streamlined than others, so I prefer to switch between them for different stages of analysis.
We will also use the treedataverse package suite for
some visualization to check in on our data quality.
treedataverse UtilityThe treedataverse suite provides tools for managing,
sharing, and visualizing phylogenetic trees in R. It builds on the
Dataverse platform to store trees (and associated data) in versioned,
citable repositories. With treedataverse, you can:
ggtree Package within the
treedataverseggtree is an extension of ggplot2 tailored
for phylogenetic trees. It lets you:
I created the functions below because I repeatedly use these code chunks to view summaries of my data after each step of processing.
my_skim <- skim_with(numeric = sfl(p25 = NULL, p50 = NULL, p75 = NULL))
skim_phyloseq <- function(phyloseq) {
options(
digits = 2,
pillar.sigfig = 2,
pillar.subtle_num = TRUE
)
skim <- psmelt(phyloseq) %>%
select(-c(
subject_certainty,
subject_studbook_id,
subject_dam_id,
subject_sire_id,
subject_birth_location,
subject_age)) %>%
group_by(subject) %>%
my_skim() %>%
select(-complete_rate)
return(skim)
}
view_tree <- function(phyloseq, level = NULL, palette = "rcartocolor::Prism") {
phylum.cols <- sample(paletteer::paletteer_d(paste0(palette)), size = length(get_taxa_unique(phyloseq, "Phylum")), replace = TRUE) %>%
set_names(., get_taxa_unique(phyloseq, "Phylum"))
tree1 <- ggtree(phyloseq, branch.length = "none", aes(color = Phylum))
if (is.null(level)) {
tree2 <- tree1
} else if (level == "Class") {
tree2 <- tree1 +
geom_label(aes(label = Class, fill = Phylum), hjust = -0.05, size = 2, colour = "#000000FF")
} else if (level == "Phylum") {
tree2 <- tree1 +
geom_label(aes(label = Phylum, fill = Phylum), hjust = -0.05, size = 3, colour = "#000000FF")
}
tree.out <- tree2 +
scale_color_manual(values = phylum.cols, na.value = "#00000080") +
scale_fill_manual( values = alpha(c(phylum.cols), 0.3)) +
theme_tree(legend.position = "none")
return(tree.out)
}
Note that I use
.RDatafiles to load some of the data below. You could load these same objects in the form of more widely applicable files, if you wish (see below for explaination).
An .RData (or sometimes .rda) file is R’s
native, binary workspace format. When you call save() on
one or more R objects—data frames, matrices, lists, S4/S3 objects,
etc.—R serializes them into a compact, platform-independent file. You
can later restore those exact objects (with their names and attributes
intact) by calling load(“your_file.RData”). Using
.RData is an efficient way to cache intermediate steps,
share processed datasets with collaborators, or speed up analyses by
skipping time-consuming recomputation.
tree <- read.tree("microeco/loris/refs_tree.treefile")
seqs <- readDNAStringSet("microeco/loris/refs_aligned_mafft.fasta")
load("microeco/loris/tax_table.RData")
load("microeco/loris/sample_table.RData")
load("microeco/loris/otu_table.RData")
Phyloseq will only capture numeric/factor values (not strings) for the metadata, so we need to reformat our character columns.
sample_data <- sample.table %>%
arrange(subject, collection_day) %>%
mutate(subject_certainty = fct_recode(subject_certainty , "0" = "no" , "1" = "yes"),
environment_holding = fct_recode(environment_holding, "0" = "old", "1" = "new"),
environment_pair_access = fct_recode(environment_pair_access, "0" = "n", "1" = "y"),
repro_warb_status = fct_recode(repro_warb_status, "0" = "anestrus", "1" = "estrus")) %>%
mutate(across(where(is.character), ~factor(.))) %>%
mutate(diet_name = fct_inorder(diet_name))
phylo <- phyloseq(
tax_table(as.matrix(tax.table)),
otu_table(as.matrix(otu.table), taxa_are_rows = TRUE),
sample_data(sample_data),
phy_tree(tree),
refseq(seqs)
)
skim_phyloseq(phylo)
| Name | Piped data |
| Number of rows | 906576 |
| Number of columns | 87 |
| _______________________ | |
| Column type frequency: | |
| character | 9 |
| Date | 1 |
| factor | 6 |
| numeric | 70 |
| ________________________ | |
| Group variables | subject |
Variable type: character
| skim_variable | subject | n_missing | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| OTU | culi | 0 | 6 | 11 | 0 | 2244 | 0 |
| OTU | warble | 0 | 6 | 11 | 0 | 2244 | 0 |
| Sample | culi | 0 | 10 | 15 | 0 | 175 | 0 |
| Sample | warble | 0 | 10 | 15 | 0 | 229 | 0 |
| Kingdom | culi | 0 | 11 | 11 | 0 | 1 | 0 |
| Kingdom | warble | 0 | 11 | 11 | 0 | 1 | 0 |
| Phylum | culi | 0 | 13 | 29 | 0 | 26 | 0 |
| Phylum | warble | 0 | 13 | 29 | 0 | 26 | 0 |
| Class | culi | 0 | 3 | 26 | 0 | 56 | 0 |
| Class | warble | 0 | 3 | 26 | 0 | 56 | 0 |
| Order | culi | 0 | 3 | 26 | 0 | 128 | 0 |
| Order | warble | 0 | 3 | 26 | 0 | 128 | 0 |
| Family | culi | 0 | 3 | 32 | 0 | 273 | 0 |
| Family | warble | 0 | 3 | 32 | 0 | 273 | 0 |
| Genus | culi | 0 | 3 | 26 | 0 | 925 | 0 |
| Genus | warble | 0 | 3 | 26 | 0 | 925 | 0 |
| Species | culi | 0 | 15 | 46 | 0 | 2244 | 0 |
| Species | warble | 0 | 15 | 46 | 0 | 2244 | 0 |
Variable type: Date
| skim_variable | subject | n_missing | min | max | median | n_unique |
|---|---|---|---|---|---|---|
| collection_date | culi | 0 | 2023-10-26 | 2024-12-14 | 2024-02-04 | 166 |
| collection_date | warble | 0 | 2023-10-26 | 2024-09-15 | 2024-03-26 | 219 |
Variable type: factor
| skim_variable | subject | n_missing | ordered | n_unique | top_counts |
|---|---|---|---|---|---|
| subject_sex | culi | 0 | FALSE | 1 | m: 392700, f: 0 |
| subject_sex | warble | 0 | FALSE | 1 | f: 513876, m: 0 |
| subject_day | culi | 0 | FALSE | 166 | cul: 4488, cul: 4488, cul: 4488, cul: 4488 |
| subject_day | warble | 0 | FALSE | 219 | war: 4488, war: 4488, war: 4488, war: 4488 |
| environment_holding | culi | 0 | FALSE | 2 | 0: 246840, 1: 145860 |
| environment_holding | warble | 0 | FALSE | 2 | 1: 302940, 0: 210936 |
| environment_pair_access | culi | 0 | FALSE | 2 | 0: 359040, 1: 33660 |
| environment_pair_access | warble | 0 | FALSE | 2 | 0: 489192, 1: 24684 |
| repro_warb_status | culi | 0 | FALSE | 3 | 0: 296208, pre: 53856, 1: 42636 |
| repro_warb_status | warble | 0 | FALSE | 3 | 0: 235620, pre: 235620, 1: 42636 |
| diet_name | culi | 0 | FALSE | 3 | oat: 249084, bas: 141372, bis: 2244 |
| diet_name | warble | 0 | FALSE | 1 | bas: 513876, oat: 0, bis: 0 |
Variable type: numeric
| skim_variable | subject | n_missing | mean | sd | p0 | p100 | hist |
|---|---|---|---|---|---|---|---|
| Abundance | culi | 0 | 3.21 | 62.37 | 0.00 | 7168.00 | ▇▁▁▁▁ |
| Abundance | warble | 0 | 2.72 | 56.75 | 0.00 | 8486.00 | ▇▁▁▁▁ |
| collection_day | culi | 0 | 100.13 | 62.10 | 1.00 | 416.00 | ▇▇▂▁▁ |
| collection_day | warble | 0 | 161.90 | 96.25 | 1.00 | 326.00 | ▇▇▇▆▇ |
| bristol_min | culi | 8976 | 3.11 | 1.03 | 0.00 | 6.00 | ▁▂▇▁▂ |
| bristol_min | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| bristol_mean | culi | 0 | 3.49 | 1.18 | 0.00 | 6.00 | ▁▃▇▅▂ |
| bristol_mean | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| bristol_max | culi | 8976 | 3.85 | 1.56 | 0.00 | 6.00 | ▁▃▇▁▇ |
| bristol_max | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| supplement_probiotic | culi | 0 | 0.71 | 0.44 | 0.00 | 1.00 | ▃▁▁▁▇ |
| supplement_probiotic | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| supplement_steroid | culi | 0 | 0.69 | 0.43 | 0.00 | 1.00 | ▃▁▂▁▇ |
| supplement_steroid | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| supplement_fiber | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| supplement_fiber | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| supplement_antibiotic | culi | 0 | 0.02 | 0.13 | 0.00 | 1.00 | ▇▁▁▁▁ |
| supplement_antibiotic | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Total_total | culi | 0 | 0.60 | 0.04 | 0.54 | 0.73 | ▅▁▇▁▁ |
| diet_Total_total | warble | 0 | 0.54 | 0.00 | 0.54 | 0.54 | ▁▁▇▁▁ |
| diet_Protein_total | culi | 0 | 0.67 | 0.02 | 0.60 | 0.69 | ▁▁▁▇▅ |
| diet_Protein_total | warble | 0 | 0.69 | 0.00 | 0.69 | 0.69 | ▁▁▇▁▁ |
| diet_Fat_total | culi | 0 | 0.62 | 0.01 | 0.61 | 0.70 | ▇▅▁▁▁ |
| diet_Fat_total | warble | 0 | 0.63 | 0.00 | 0.63 | 0.63 | ▁▁▇▁▁ |
| diet_CHO_by_diff_total | culi | 0 | 0.34 | 0.04 | 0.29 | 0.60 | ▅▇▁▁▁ |
| diet_CHO_by_diff_total | warble | 0 | 0.29 | 0.00 | 0.29 | 0.29 | ▁▁▇▁▁ |
| diet_Ash_total | culi | 0 | 1.00 | 0.02 | 0.79 | 1.00 | ▁▁▁▁▇ |
| diet_Ash_total | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Total_dry_matter | culi | 0 | 0.56 | 0.01 | 0.53 | 0.56 | ▁▁▁▅▇ |
| diet_Total_dry_matter | warble | 0 | 0.55 | 0.00 | 0.55 | 0.55 | ▁▁▇▁▁ |
| diet_Total_kcal | culi | 0 | 0.97 | 0.00 | 0.97 | 0.97 | ▁▁▇▁▁ |
| diet_Total_kcal | warble | 0 | 0.97 | 0.00 | 0.97 | 0.97 | ▁▁▇▁▁ |
| diet_Foods_biscuit_rotation | culi | 0 | 0.23 | 0.02 | 0.00 | 0.25 | ▁▁▁▁▇ |
| diet_Foods_biscuit_rotation | warble | 0 | 0.25 | 0.00 | 0.25 | 0.25 | ▁▁▇▁▁ |
| diet_Foods_invertebrate_misc | culi | 0 | 0.15 | 0.03 | 0.13 | 0.26 | ▇▁▅▁▁ |
| diet_Foods_invertebrate_misc | warble | 0 | 0.19 | 0.00 | 0.19 | 0.19 | ▁▁▇▁▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | culi | 0 | 0.21 | 0.01 | 0.20 | 0.24 | ▇▁▁▅▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | warble | 0 | 0.23 | 0.00 | 0.23 | 0.23 | ▁▁▇▁▁ |
| diet_Foods_protein_rotation | culi | 0 | 0.04 | 0.00 | 0.04 | 0.07 | ▇▁▁▁▁ |
| diet_Foods_protein_rotation | warble | 0 | 0.04 | 0.00 | 0.04 | 0.04 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables | culi | 0 | 0.32 | 0.02 | 0.29 | 0.43 | ▅▇▁▁▁ |
| diet_Foods_seasonal_vegetables | warble | 0 | 0.29 | 0.00 | 0.29 | 0.29 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_carrot | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_carrot | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_celery | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_celery | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | culi | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Foods_ohdz_oatmeal_gel | culi | 0 | 0.05 | 0.04 | 0.00 | 0.08 | ▅▁▁▁▇ |
| diet_Foods_ohdz_oatmeal_gel | warble | 0 | 0.00 | 0.00 | 0.00 | 0.00 | ▁▁▇▁▁ |
| diet_Protein_taurine | culi | 0 | 0.99 | 0.08 | 0.00 | 1.00 | ▁▁▁▁▇ |
| diet_Protein_taurine | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Protein_methionine | culi | 0 | 0.44 | 0.01 | 0.32 | 0.45 | ▁▁▁▁▇ |
| diet_Protein_methionine | warble | 0 | 0.45 | 0.00 | 0.45 | 0.45 | ▁▁▇▁▁ |
| diet_Fat_omega_3_ala__epa__dha | culi | 0 | 0.99 | 0.08 | 0.00 | 1.00 | ▁▁▁▁▇ |
| diet_Fat_omega_3_ala__epa__dha | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Fat_omega_6_la__gla__aa | culi | 0 | 0.99 | 0.08 | 0.00 | 1.00 | ▁▁▁▁▇ |
| diet_Fat_omega_6_la__gla__aa | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_CHO_by_diff_starch | culi | 0 | 0.95 | 0.07 | 0.38 | 1.00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_starch | warble | 0 | 0.88 | 0.00 | 0.88 | 0.88 | ▁▁▇▁▁ |
| diet_CHO_by_diff_ndf | culi | 0 | 0.78 | 0.01 | 0.75 | 0.78 | ▁▁▅▁▇ |
| diet_CHO_by_diff_ndf | warble | 0 | 0.77 | 0.00 | 0.77 | 0.77 | ▁▁▇▁▁ |
| diet_CHO_by_diff_adf | culi | 0 | 0.99 | 0.05 | 0.31 | 1.00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_adf | warble | 0 | 0.97 | 0.00 | 0.97 | 0.97 | ▁▁▇▁▁ |
| diet_CHO_by_diff_crude_fiber | culi | 0 | 0.57 | 0.01 | 0.57 | 0.71 | ▇▁▁▁▁ |
| diet_CHO_by_diff_crude_fiber | warble | 0 | 0.57 | 0.00 | 0.57 | 0.57 | ▁▁▇▁▁ |
| diet_CHO_by_diff_tdf | culi | 0 | 0.41 | 0.04 | 0.38 | 0.76 | ▇▁▁▁▁ |
| diet_CHO_by_diff_tdf | warble | 0 | 0.38 | 0.00 | 0.38 | 0.38 | ▁▁▇▁▁ |
| diet_Ash_calcium | culi | 0 | 0.96 | 0.01 | 0.77 | 0.97 | ▁▁▁▁▇ |
| diet_Ash_calcium | warble | 0 | 0.97 | 0.00 | 0.97 | 0.97 | ▁▁▇▁▁ |
| diet_Ash_phosphorus | culi | 0 | 0.96 | 0.03 | 0.94 | 1.00 | ▇▁▁▁▅ |
| diet_Ash_phosphorus | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Ash_potassium | culi | 0 | 0.88 | 0.00 | 0.88 | 0.91 | ▇▁▁▁▁ |
| diet_Ash_potassium | warble | 0 | 0.88 | 0.00 | 0.88 | 0.88 | ▁▁▇▁▁ |
| diet_Ash_magnesium | culi | 0 | 0.50 | 0.05 | 0.44 | 0.72 | ▅▇▁▁▁ |
| diet_Ash_magnesium | warble | 0 | 0.44 | 0.00 | 0.44 | 0.44 | ▁▁▇▁▁ |
| diet_Ash_copper | culi | 0 | 0.99 | 0.05 | 0.31 | 1.00 | ▁▁▁▁▇ |
| diet_Ash_copper | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Ash_iron | culi | 0 | 0.98 | 0.02 | 0.79 | 1.00 | ▁▁▁▁▇ |
| diet_Ash_iron | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Ash_zinc | culi | 0 | 0.98 | 0.04 | 0.47 | 1.00 | ▁▁▁▁▇ |
| diet_Ash_zinc | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Ash_manganese | culi | 0 | 0.99 | 0.06 | 0.24 | 1.00 | ▁▁▁▁▇ |
| diet_Ash_manganese | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Ash_iodine | culi | 0 | 0.99 | 0.08 | 0.00 | 1.00 | ▁▁▁▁▇ |
| diet_Ash_iodine | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Ash_ca_p | culi | 0 | 0.84 | 0.02 | 0.69 | 0.86 | ▁▁▁▅▇ |
| diet_Ash_ca_p | warble | 0 | 0.81 | 0.00 | 0.81 | 0.81 | ▁▁▇▁▁ |
| diet_Vitamins_vit_a_iu | culi | 0 | 0.25 | 0.02 | 0.23 | 0.27 | ▅▁▁▁▇ |
| diet_Vitamins_vit_a_iu | warble | 0 | 0.23 | 0.00 | 0.23 | 0.23 | ▁▁▇▁▁ |
| diet_Vitamins_vit_d3 | culi | 0 | 0.98 | 0.02 | 0.73 | 0.98 | ▁▁▁▁▇ |
| diet_Vitamins_vit_d3 | warble | 0 | 0.98 | 0.00 | 0.98 | 0.98 | ▁▁▇▁▁ |
| diet_Vitamins_vit_e | culi | 0 | 0.93 | 0.10 | 0.64 | 1.00 | ▁▁▅▁▇ |
| diet_Vitamins_vit_e | warble | 0 | 0.80 | 0.00 | 0.80 | 0.80 | ▁▁▇▁▁ |
| diet_Vitamins_vit_k | culi | 0 | 0.97 | 0.04 | 0.40 | 0.98 | ▁▁▁▁▇ |
| diet_Vitamins_vit_k | warble | 0 | 0.96 | 0.00 | 0.96 | 0.96 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b1_thiamin | culi | 0 | 0.98 | 0.05 | 0.28 | 0.99 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b1_thiamin | warble | 0 | 0.98 | 0.00 | 0.98 | 0.98 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b2_riboflavin | culi | 0 | 0.91 | 0.03 | 0.68 | 0.94 | ▁▁▁▇▅ |
| diet_Vitamins_vit_b2_riboflavin | warble | 0 | 0.94 | 0.00 | 0.94 | 0.94 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b3_niacin | culi | 0 | 0.99 | 0.04 | 0.49 | 1.00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b3_niacin | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Vitamins_choline | culi | 0 | 0.50 | 0.01 | 0.46 | 0.52 | ▁▁▇▁▅ |
| diet_Vitamins_choline | warble | 0 | 0.52 | 0.00 | 0.52 | 0.52 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b5_pantothenic_acid | culi | 0 | 0.92 | 0.04 | 0.39 | 0.94 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b5_pantothenic_acid | warble | 0 | 0.94 | 0.00 | 0.94 | 0.94 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b6_pyridoxine | culi | 0 | 0.96 | 0.05 | 0.35 | 0.96 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b6_pyridoxine | warble | 0 | 0.96 | 0.00 | 0.96 | 0.96 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b7_biotin | culi | 0 | 0.99 | 0.02 | 0.72 | 1.00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b7_biotin | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Vitamins_folic_acid | culi | 0 | 0.99 | 0.07 | 0.05 | 1.00 | ▁▁▁▁▇ |
| diet_Vitamins_folic_acid | warble | 0 | 1.00 | 0.00 | 1.00 | 1.00 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b12 | culi | 0 | 0.50 | 0.07 | 0.45 | 1.00 | ▇▅▁▁▁ |
| diet_Vitamins_vit_b12 | warble | 0 | 0.56 | 0.00 | 0.56 | 0.56 | ▁▁▇▁▁ |
| diet_Vitamins_vit_c | culi | 0 | 0.97 | 0.04 | 0.65 | 1.00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_c | warble | 0 | 0.93 | 0.00 | 0.93 | 0.93 | ▁▁▇▁▁ |
| diet_Vitamins_beta_carotene | culi | 0 | 0.21 | 0.02 | 0.18 | 0.24 | ▅▁▁▇▁ |
| diet_Vitamins_beta_carotene | warble | 0 | 0.18 | 0.00 | 0.18 | 0.18 | ▁▁▇▁▁ |
| diet_Vitamins_lycopene | culi | 0 | 0.40 | 0.06 | 0.32 | 0.65 | ▅▇▁▁▁ |
| diet_Vitamins_lycopene | warble | 0 | 0.32 | 0.00 | 0.32 | 0.32 | ▁▁▇▁▁ |
view_tree(phylo) + ggtitle("Species-Level OTUs before Filtering")
That looks like some very dense, messy taxonomic data!
First we will create a version that merges the replicated samples so that we have one observation per subject per day. This function’s default in phyloseq will aggregate the OTU counts across multiple samples as a sum of reads while taking mean values for everything in the metadata.
This pooling step creates one composite sample per subject per day, avoiding pseudo‐replication in downstream diversity metrics.
phylo_merged <- phylo %>% merge_samples("subject_day")
skim_phyloseq(phylo_merged)
| Name | Piped data |
| Number of rows | 863940 |
| Number of columns | 87 |
| _______________________ | |
| Column type frequency: | |
| character | 9 |
| numeric | 77 |
| ________________________ | |
| Group variables | subject |
Variable type: character
| skim_variable | subject | n_missing | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| OTU | 1 | 0 | 6 | 11 | 0 | 2244 | 0 |
| OTU | 2 | 0 | 6 | 11 | 0 | 2244 | 0 |
| Sample | 1 | 0 | 6 | 8 | 0 | 166 | 0 |
| Sample | 2 | 0 | 8 | 10 | 0 | 219 | 0 |
| Kingdom | 1 | 0 | 11 | 11 | 0 | 1 | 0 |
| Kingdom | 2 | 0 | 11 | 11 | 0 | 1 | 0 |
| Phylum | 1 | 0 | 13 | 29 | 0 | 26 | 0 |
| Phylum | 2 | 0 | 13 | 29 | 0 | 26 | 0 |
| Class | 1 | 0 | 3 | 26 | 0 | 56 | 0 |
| Class | 2 | 0 | 3 | 26 | 0 | 56 | 0 |
| Order | 1 | 0 | 3 | 26 | 0 | 128 | 0 |
| Order | 2 | 0 | 3 | 26 | 0 | 128 | 0 |
| Family | 1 | 0 | 3 | 32 | 0 | 273 | 0 |
| Family | 2 | 0 | 3 | 32 | 0 | 273 | 0 |
| Genus | 1 | 0 | 3 | 26 | 0 | 925 | 0 |
| Genus | 2 | 0 | 3 | 26 | 0 | 925 | 0 |
| Species | 1 | 0 | 15 | 46 | 0 | 2244 | 0 |
| Species | 2 | 0 | 15 | 46 | 0 | 2244 | 0 |
Variable type: numeric
| skim_variable | subject | n_missing | mean | sd | p0 | p100 | hist |
|---|---|---|---|---|---|---|---|
| Abundance | 1 | 0 | 3.4e+00 | 65.57 | 0.0e+00 | 7.2e+03 | ▇▁▁▁▁ |
| Abundance | 2 | 0 | 2.9e+00 | 58.71 | 0.0e+00 | 8.5e+03 | ▇▁▁▁▁ |
| subject_sex | 1 | 0 | 2.0e+00 | 0.00 | 2.0e+00 | 2.0e+00 | ▁▁▇▁▁ |
| subject_sex | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| subject_day | 1 | 0 | 8.4e+01 | 47.92 | 1.0e+00 | 1.7e+02 | ▇▇▇▇▇ |
| subject_day | 2 | 0 | 2.8e+02 | 63.22 | 1.7e+02 | 3.8e+02 | ▇▇▇▇▇ |
| collection_day | 1 | 0 | 1.0e+02 | 62.09 | 1.0e+00 | 4.2e+02 | ▇▇▂▁▁ |
| collection_day | 2 | 0 | 1.6e+02 | 95.94 | 1.0e+00 | 3.3e+02 | ▇▇▇▆▇ |
| collection_date | 1 | 0 | 2.0e+04 | 62.09 | 2.0e+04 | 2.0e+04 | ▇▇▂▁▁ |
| collection_date | 2 | 0 | 2.0e+04 | 95.94 | 2.0e+04 | 2.0e+04 | ▇▇▇▆▇ |
| environment_holding | 1 | 0 | 1.6e+00 | 0.48 | 1.0e+00 | 2.0e+00 | ▅▁▁▁▇ |
| environment_holding | 2 | 0 | 1.4e+00 | 0.49 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▆ |
| environment_pair_access | 1 | 0 | 1.1e+00 | 0.29 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| environment_pair_access | 2 | 0 | 1.1e+00 | 0.22 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| repro_warb_status | 1 | 0 | 1.4e+00 | 0.73 | 1.0e+00 | 3.0e+00 | ▇▁▁▁▂ |
| repro_warb_status | 2 | 0 | 2.0e+00 | 0.96 | 1.0e+00 | 3.0e+00 | ▇▁▂▁▇ |
| bristol_min | 1 | 8976 | 3.1e+00 | 1.02 | 0.0e+00 | 6.0e+00 | ▁▂▇▁▂ |
| bristol_min | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_mean | 1 | 0 | 3.5e+00 | 1.17 | 0.0e+00 | 6.0e+00 | ▁▃▇▃▂ |
| bristol_mean | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_max | 1 | 8976 | 3.8e+00 | 1.55 | 0.0e+00 | 6.0e+00 | ▁▃▇▁▆ |
| bristol_max | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| supplement_probiotic | 1 | 0 | 7.1e-01 | 0.44 | 0.0e+00 | 1.0e+00 | ▃▁▁▁▇ |
| supplement_probiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_steroid | 1 | 0 | 7.0e-01 | 0.43 | 0.0e+00 | 1.0e+00 | ▃▁▂▁▇ |
| supplement_steroid | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antibiotic | 1 | 0 | 2.0e-02 | 0.13 | 0.0e+00 | 1.0e+00 | ▇▁▁▁▁ |
| supplement_antibiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_name | 1 | 0 | 1.7e+00 | 0.49 | 1.0e+00 | 3.0e+00 | ▅▁▇▁▁ |
| diet_name | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_total | 1 | 0 | 6.0e-01 | 0.04 | 5.4e-01 | 7.3e-01 | ▅▁▇▁▁ |
| diet_Total_total | 2 | 0 | 5.4e-01 | 0.00 | 5.4e-01 | 5.4e-01 | ▁▁▇▁▁ |
| diet_Protein_total | 1 | 0 | 6.7e-01 | 0.02 | 6.0e-01 | 6.9e-01 | ▁▁▁▇▅ |
| diet_Protein_total | 2 | 0 | 6.9e-01 | 0.00 | 6.9e-01 | 6.9e-01 | ▁▁▇▁▁ |
| diet_Fat_total | 1 | 0 | 6.2e-01 | 0.01 | 6.1e-01 | 7.0e-01 | ▇▅▁▁▁ |
| diet_Fat_total | 2 | 0 | 6.3e-01 | 0.00 | 6.3e-01 | 6.3e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_total | 1 | 0 | 3.4e-01 | 0.04 | 2.9e-01 | 6.0e-01 | ▅▇▁▁▁ |
| diet_CHO_by_diff_total | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Ash_total | 1 | 0 | 1.0e+00 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_total | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_dry_matter | 1 | 0 | 5.6e-01 | 0.01 | 5.3e-01 | 5.6e-01 | ▁▁▁▅▇ |
| diet_Total_dry_matter | 2 | 0 | 5.5e-01 | 0.00 | 5.5e-01 | 5.5e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 1 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Foods_biscuit_rotation | 1 | 0 | 2.3e-01 | 0.02 | 0.0e+00 | 2.5e-01 | ▁▁▁▁▇ |
| diet_Foods_biscuit_rotation | 2 | 0 | 2.5e-01 | 0.00 | 2.5e-01 | 2.5e-01 | ▁▁▇▁▁ |
| diet_Foods_invertebrate_misc | 1 | 0 | 1.5e-01 | 0.03 | 1.3e-01 | 2.6e-01 | ▇▁▅▁▁ |
| diet_Foods_invertebrate_misc | 2 | 0 | 1.9e-01 | 0.00 | 1.9e-01 | 1.9e-01 | ▁▁▇▁▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 1 | 0 | 2.1e-01 | 0.01 | 2.0e-01 | 2.4e-01 | ▇▁▁▅▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Foods_protein_rotation | 1 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 7.0e-02 | ▇▁▁▁▁ |
| diet_Foods_protein_rotation | 2 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 4.0e-02 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables | 1 | 0 | 3.2e-01 | 0.02 | 2.9e-01 | 4.3e-01 | ▅▇▁▁▁ |
| diet_Foods_seasonal_vegetables | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_ohdz_oatmeal_gel | 1 | 0 | 5.0e-02 | 0.04 | 0.0e+00 | 8.0e-02 | ▅▁▁▁▇ |
| diet_Foods_ohdz_oatmeal_gel | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Protein_taurine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Protein_taurine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Protein_methionine | 1 | 0 | 4.4e-01 | 0.01 | 3.2e-01 | 4.5e-01 | ▁▁▁▁▇ |
| diet_Protein_methionine | 2 | 0 | 4.5e-01 | 0.00 | 4.5e-01 | 4.5e-01 | ▁▁▇▁▁ |
| diet_Fat_omega_3_ala__epa__dha | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_3_ala__epa__dha | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Fat_omega_6_la__gla__aa | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_6_la__gla__aa | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_CHO_by_diff_starch | 1 | 0 | 9.5e-01 | 0.07 | 3.8e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_starch | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_ndf | 1 | 0 | 7.8e-01 | 0.01 | 7.5e-01 | 7.8e-01 | ▁▁▅▁▇ |
| diet_CHO_by_diff_ndf | 2 | 0 | 7.7e-01 | 0.00 | 7.7e-01 | 7.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_adf | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_adf | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_crude_fiber | 1 | 0 | 5.7e-01 | 0.01 | 5.7e-01 | 7.1e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_crude_fiber | 2 | 0 | 5.7e-01 | 0.00 | 5.7e-01 | 5.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_tdf | 1 | 0 | 4.1e-01 | 0.04 | 3.8e-01 | 7.6e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_tdf | 2 | 0 | 3.8e-01 | 0.00 | 3.8e-01 | 3.8e-01 | ▁▁▇▁▁ |
| diet_Ash_calcium | 1 | 0 | 9.6e-01 | 0.01 | 7.7e-01 | 9.7e-01 | ▁▁▁▁▇ |
| diet_Ash_calcium | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Ash_phosphorus | 1 | 0 | 9.6e-01 | 0.03 | 9.4e-01 | 1.0e+00 | ▇▁▁▁▅ |
| diet_Ash_phosphorus | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_potassium | 1 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 9.1e-01 | ▇▁▁▁▁ |
| diet_Ash_potassium | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_Ash_magnesium | 1 | 0 | 5.0e-01 | 0.05 | 4.4e-01 | 7.2e-01 | ▅▇▁▁▁ |
| diet_Ash_magnesium | 2 | 0 | 4.4e-01 | 0.00 | 4.4e-01 | 4.4e-01 | ▁▁▇▁▁ |
| diet_Ash_copper | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_copper | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iron | 1 | 0 | 9.8e-01 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iron | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_zinc | 1 | 0 | 9.8e-01 | 0.04 | 4.7e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_zinc | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_manganese | 1 | 0 | 9.9e-01 | 0.06 | 2.4e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_manganese | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iodine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iodine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_ca_p | 1 | 0 | 8.4e-01 | 0.02 | 6.9e-01 | 8.6e-01 | ▁▁▁▅▇ |
| diet_Ash_ca_p | 2 | 0 | 8.1e-01 | 0.00 | 8.1e-01 | 8.1e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_a_iu | 1 | 0 | 2.5e-01 | 0.02 | 2.3e-01 | 2.7e-01 | ▅▁▁▁▇ |
| diet_Vitamins_vit_a_iu | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_d3 | 1 | 0 | 9.8e-01 | 0.02 | 7.3e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_d3 | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_e | 1 | 0 | 9.3e-01 | 0.10 | 6.4e-01 | 1.0e+00 | ▁▁▅▁▇ |
| diet_Vitamins_vit_e | 2 | 0 | 8.0e-01 | 0.00 | 8.0e-01 | 8.0e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_k | 1 | 0 | 9.7e-01 | 0.04 | 4.0e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_k | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b1_thiamin | 1 | 0 | 9.8e-01 | 0.06 | 2.8e-01 | 9.9e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b1_thiamin | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b2_riboflavin | 1 | 0 | 9.0e-01 | 0.03 | 6.8e-01 | 9.4e-01 | ▁▁▁▇▅ |
| diet_Vitamins_vit_b2_riboflavin | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b3_niacin | 1 | 0 | 9.9e-01 | 0.04 | 4.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b3_niacin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_choline | 1 | 0 | 5.0e-01 | 0.01 | 4.6e-01 | 5.2e-01 | ▁▁▇▁▅ |
| diet_Vitamins_choline | 2 | 0 | 5.2e-01 | 0.00 | 5.2e-01 | 5.2e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b5_pantothenic_acid | 1 | 0 | 9.2e-01 | 0.04 | 3.9e-01 | 9.4e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b5_pantothenic_acid | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b6_pyridoxine | 1 | 0 | 9.6e-01 | 0.05 | 3.5e-01 | 9.6e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b6_pyridoxine | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b7_biotin | 1 | 0 | 9.9e-01 | 0.02 | 7.2e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b7_biotin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_folic_acid | 1 | 0 | 9.9e-01 | 0.07 | 5.0e-02 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_folic_acid | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b12 | 1 | 0 | 4.9e-01 | 0.07 | 4.5e-01 | 1.0e+00 | ▇▅▁▁▁ |
| diet_Vitamins_vit_b12 | 2 | 0 | 5.6e-01 | 0.00 | 5.6e-01 | 5.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_c | 1 | 0 | 9.7e-01 | 0.04 | 6.5e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_c | 2 | 0 | 9.3e-01 | 0.00 | 9.3e-01 | 9.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_beta_carotene | 1 | 0 | 2.1e-01 | 0.02 | 1.8e-01 | 2.4e-01 | ▅▁▁▇▁ |
| diet_Vitamins_beta_carotene | 2 | 0 | 1.8e-01 | 0.00 | 1.8e-01 | 1.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_lycopene | 1 | 0 | 4.0e-01 | 0.06 | 3.2e-01 | 6.5e-01 | ▅▇▁▁▁ |
| diet_Vitamins_lycopene | 2 | 0 | 3.2e-01 | 0.00 | 3.2e-01 | 3.2e-01 | ▁▁▇▁▁ |
Drop the OTUs with the lowest abundances. Constraining your dataset to taxa with >1 total read helps stabilize diversity estimates and speeds up tree operations.
First let’s see how many OTUs we lose at different thresholds
rare_otus <- names(taxa_sums(phylo_merged)[taxa_sums(phylo_merged) <= 1])
keep_otus <- names(taxa_sums(phylo_merged)[taxa_sums(phylo_merged) > 1])
length(rare_otus)
[1] 599
length(keep_otus)
[1] 1645
We will remove 599 otus where the total abundance is less than or
equal to 1 and keep the 1645 otus with a total abundance of at least 2.
(You can change the value in the keep_otus function
above to use a higher/lower threshold.)
phylo_pruned <- prune_taxa(keep_otus, phylo_merged)
skim_phyloseq(phylo_pruned)
| Name | Piped data |
| Number of rows | 633325 |
| Number of columns | 87 |
| _______________________ | |
| Column type frequency: | |
| character | 9 |
| numeric | 77 |
| ________________________ | |
| Group variables | subject |
Variable type: character
| skim_variable | subject | n_missing | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| OTU | 1 | 0 | 6 | 11 | 0 | 1645 | 0 |
| OTU | 2 | 0 | 6 | 11 | 0 | 1645 | 0 |
| Sample | 1 | 0 | 6 | 8 | 0 | 166 | 0 |
| Sample | 2 | 0 | 8 | 10 | 0 | 219 | 0 |
| Kingdom | 1 | 0 | 11 | 11 | 0 | 1 | 0 |
| Kingdom | 2 | 0 | 11 | 11 | 0 | 1 | 0 |
| Phylum | 1 | 0 | 13 | 29 | 0 | 25 | 0 |
| Phylum | 2 | 0 | 13 | 29 | 0 | 25 | 0 |
| Class | 1 | 0 | 3 | 24 | 0 | 51 | 0 |
| Class | 2 | 0 | 3 | 24 | 0 | 51 | 0 |
| Order | 1 | 0 | 3 | 26 | 0 | 105 | 0 |
| Order | 2 | 0 | 3 | 26 | 0 | 105 | 0 |
| Family | 1 | 0 | 3 | 32 | 0 | 218 | 0 |
| Family | 2 | 0 | 3 | 32 | 0 | 218 | 0 |
| Genus | 1 | 0 | 3 | 26 | 0 | 699 | 0 |
| Genus | 2 | 0 | 3 | 26 | 0 | 699 | 0 |
| Species | 1 | 0 | 15 | 46 | 0 | 1645 | 0 |
| Species | 2 | 0 | 15 | 46 | 0 | 1645 | 0 |
Variable type: numeric
| skim_variable | subject | n_missing | mean | sd | p0 | p100 | hist |
|---|---|---|---|---|---|---|---|
| Abundance | 1 | 0 | 4.6e+00 | 76.55 | 0.0e+00 | 7.2e+03 | ▇▁▁▁▁ |
| Abundance | 2 | 0 | 3.9e+00 | 68.54 | 0.0e+00 | 8.5e+03 | ▇▁▁▁▁ |
| subject_sex | 1 | 0 | 2.0e+00 | 0.00 | 2.0e+00 | 2.0e+00 | ▁▁▇▁▁ |
| subject_sex | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| subject_day | 1 | 0 | 8.4e+01 | 47.92 | 1.0e+00 | 1.7e+02 | ▇▇▇▇▇ |
| subject_day | 2 | 0 | 2.8e+02 | 63.22 | 1.7e+02 | 3.8e+02 | ▇▇▇▇▇ |
| collection_day | 1 | 0 | 1.0e+02 | 62.09 | 1.0e+00 | 4.2e+02 | ▇▇▂▁▁ |
| collection_day | 2 | 0 | 1.6e+02 | 95.94 | 1.0e+00 | 3.3e+02 | ▇▇▇▆▇ |
| collection_date | 1 | 0 | 2.0e+04 | 62.09 | 2.0e+04 | 2.0e+04 | ▇▇▂▁▁ |
| collection_date | 2 | 0 | 2.0e+04 | 95.94 | 2.0e+04 | 2.0e+04 | ▇▇▇▆▇ |
| environment_holding | 1 | 0 | 1.6e+00 | 0.48 | 1.0e+00 | 2.0e+00 | ▅▁▁▁▇ |
| environment_holding | 2 | 0 | 1.4e+00 | 0.49 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▆ |
| environment_pair_access | 1 | 0 | 1.1e+00 | 0.29 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| environment_pair_access | 2 | 0 | 1.1e+00 | 0.22 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| repro_warb_status | 1 | 0 | 1.4e+00 | 0.73 | 1.0e+00 | 3.0e+00 | ▇▁▁▁▂ |
| repro_warb_status | 2 | 0 | 2.0e+00 | 0.96 | 1.0e+00 | 3.0e+00 | ▇▁▂▁▇ |
| bristol_min | 1 | 6580 | 3.1e+00 | 1.02 | 0.0e+00 | 6.0e+00 | ▁▂▇▁▂ |
| bristol_min | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_mean | 1 | 0 | 3.5e+00 | 1.17 | 0.0e+00 | 6.0e+00 | ▁▃▇▃▂ |
| bristol_mean | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_max | 1 | 6580 | 3.8e+00 | 1.55 | 0.0e+00 | 6.0e+00 | ▁▃▇▁▆ |
| bristol_max | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| supplement_probiotic | 1 | 0 | 7.1e-01 | 0.44 | 0.0e+00 | 1.0e+00 | ▃▁▁▁▇ |
| supplement_probiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_steroid | 1 | 0 | 7.0e-01 | 0.43 | 0.0e+00 | 1.0e+00 | ▃▁▂▁▇ |
| supplement_steroid | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antibiotic | 1 | 0 | 2.0e-02 | 0.13 | 0.0e+00 | 1.0e+00 | ▇▁▁▁▁ |
| supplement_antibiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_name | 1 | 0 | 1.7e+00 | 0.49 | 1.0e+00 | 3.0e+00 | ▅▁▇▁▁ |
| diet_name | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_total | 1 | 0 | 6.0e-01 | 0.04 | 5.4e-01 | 7.3e-01 | ▅▁▇▁▁ |
| diet_Total_total | 2 | 0 | 5.4e-01 | 0.00 | 5.4e-01 | 5.4e-01 | ▁▁▇▁▁ |
| diet_Protein_total | 1 | 0 | 6.7e-01 | 0.02 | 6.0e-01 | 6.9e-01 | ▁▁▁▇▅ |
| diet_Protein_total | 2 | 0 | 6.9e-01 | 0.00 | 6.9e-01 | 6.9e-01 | ▁▁▇▁▁ |
| diet_Fat_total | 1 | 0 | 6.2e-01 | 0.01 | 6.1e-01 | 7.0e-01 | ▇▅▁▁▁ |
| diet_Fat_total | 2 | 0 | 6.3e-01 | 0.00 | 6.3e-01 | 6.3e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_total | 1 | 0 | 3.4e-01 | 0.04 | 2.9e-01 | 6.0e-01 | ▅▇▁▁▁ |
| diet_CHO_by_diff_total | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Ash_total | 1 | 0 | 1.0e+00 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_total | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_dry_matter | 1 | 0 | 5.6e-01 | 0.01 | 5.3e-01 | 5.6e-01 | ▁▁▁▅▇ |
| diet_Total_dry_matter | 2 | 0 | 5.5e-01 | 0.00 | 5.5e-01 | 5.5e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 1 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Foods_biscuit_rotation | 1 | 0 | 2.3e-01 | 0.02 | 0.0e+00 | 2.5e-01 | ▁▁▁▁▇ |
| diet_Foods_biscuit_rotation | 2 | 0 | 2.5e-01 | 0.00 | 2.5e-01 | 2.5e-01 | ▁▁▇▁▁ |
| diet_Foods_invertebrate_misc | 1 | 0 | 1.5e-01 | 0.03 | 1.3e-01 | 2.6e-01 | ▇▁▅▁▁ |
| diet_Foods_invertebrate_misc | 2 | 0 | 1.9e-01 | 0.00 | 1.9e-01 | 1.9e-01 | ▁▁▇▁▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 1 | 0 | 2.1e-01 | 0.01 | 2.0e-01 | 2.4e-01 | ▇▁▁▅▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Foods_protein_rotation | 1 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 7.0e-02 | ▇▁▁▁▁ |
| diet_Foods_protein_rotation | 2 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 4.0e-02 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables | 1 | 0 | 3.2e-01 | 0.02 | 2.9e-01 | 4.3e-01 | ▅▇▁▁▁ |
| diet_Foods_seasonal_vegetables | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_ohdz_oatmeal_gel | 1 | 0 | 5.0e-02 | 0.04 | 0.0e+00 | 8.0e-02 | ▅▁▁▁▇ |
| diet_Foods_ohdz_oatmeal_gel | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Protein_taurine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Protein_taurine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Protein_methionine | 1 | 0 | 4.4e-01 | 0.01 | 3.2e-01 | 4.5e-01 | ▁▁▁▁▇ |
| diet_Protein_methionine | 2 | 0 | 4.5e-01 | 0.00 | 4.5e-01 | 4.5e-01 | ▁▁▇▁▁ |
| diet_Fat_omega_3_ala__epa__dha | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_3_ala__epa__dha | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Fat_omega_6_la__gla__aa | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_6_la__gla__aa | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_CHO_by_diff_starch | 1 | 0 | 9.5e-01 | 0.07 | 3.8e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_starch | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_ndf | 1 | 0 | 7.8e-01 | 0.01 | 7.5e-01 | 7.8e-01 | ▁▁▅▁▇ |
| diet_CHO_by_diff_ndf | 2 | 0 | 7.7e-01 | 0.00 | 7.7e-01 | 7.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_adf | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_adf | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_crude_fiber | 1 | 0 | 5.7e-01 | 0.01 | 5.7e-01 | 7.1e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_crude_fiber | 2 | 0 | 5.7e-01 | 0.00 | 5.7e-01 | 5.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_tdf | 1 | 0 | 4.1e-01 | 0.04 | 3.8e-01 | 7.6e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_tdf | 2 | 0 | 3.8e-01 | 0.00 | 3.8e-01 | 3.8e-01 | ▁▁▇▁▁ |
| diet_Ash_calcium | 1 | 0 | 9.6e-01 | 0.01 | 7.7e-01 | 9.7e-01 | ▁▁▁▁▇ |
| diet_Ash_calcium | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Ash_phosphorus | 1 | 0 | 9.6e-01 | 0.03 | 9.4e-01 | 1.0e+00 | ▇▁▁▁▅ |
| diet_Ash_phosphorus | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_potassium | 1 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 9.1e-01 | ▇▁▁▁▁ |
| diet_Ash_potassium | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_Ash_magnesium | 1 | 0 | 5.0e-01 | 0.05 | 4.4e-01 | 7.2e-01 | ▅▇▁▁▁ |
| diet_Ash_magnesium | 2 | 0 | 4.4e-01 | 0.00 | 4.4e-01 | 4.4e-01 | ▁▁▇▁▁ |
| diet_Ash_copper | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_copper | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iron | 1 | 0 | 9.8e-01 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iron | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_zinc | 1 | 0 | 9.8e-01 | 0.04 | 4.7e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_zinc | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_manganese | 1 | 0 | 9.9e-01 | 0.06 | 2.4e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_manganese | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iodine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iodine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_ca_p | 1 | 0 | 8.4e-01 | 0.02 | 6.9e-01 | 8.6e-01 | ▁▁▁▅▇ |
| diet_Ash_ca_p | 2 | 0 | 8.1e-01 | 0.00 | 8.1e-01 | 8.1e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_a_iu | 1 | 0 | 2.5e-01 | 0.02 | 2.3e-01 | 2.7e-01 | ▅▁▁▁▇ |
| diet_Vitamins_vit_a_iu | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_d3 | 1 | 0 | 9.8e-01 | 0.02 | 7.3e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_d3 | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_e | 1 | 0 | 9.3e-01 | 0.10 | 6.4e-01 | 1.0e+00 | ▁▁▅▁▇ |
| diet_Vitamins_vit_e | 2 | 0 | 8.0e-01 | 0.00 | 8.0e-01 | 8.0e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_k | 1 | 0 | 9.7e-01 | 0.04 | 4.0e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_k | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b1_thiamin | 1 | 0 | 9.8e-01 | 0.06 | 2.8e-01 | 9.9e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b1_thiamin | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b2_riboflavin | 1 | 0 | 9.0e-01 | 0.03 | 6.8e-01 | 9.4e-01 | ▁▁▁▇▅ |
| diet_Vitamins_vit_b2_riboflavin | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b3_niacin | 1 | 0 | 9.9e-01 | 0.04 | 4.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b3_niacin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_choline | 1 | 0 | 5.0e-01 | 0.01 | 4.6e-01 | 5.2e-01 | ▁▁▇▁▅ |
| diet_Vitamins_choline | 2 | 0 | 5.2e-01 | 0.00 | 5.2e-01 | 5.2e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b5_pantothenic_acid | 1 | 0 | 9.2e-01 | 0.04 | 3.9e-01 | 9.4e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b5_pantothenic_acid | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b6_pyridoxine | 1 | 0 | 9.6e-01 | 0.05 | 3.5e-01 | 9.6e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b6_pyridoxine | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b7_biotin | 1 | 0 | 9.9e-01 | 0.02 | 7.2e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b7_biotin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_folic_acid | 1 | 0 | 9.9e-01 | 0.07 | 5.0e-02 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_folic_acid | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b12 | 1 | 0 | 4.9e-01 | 0.07 | 4.5e-01 | 1.0e+00 | ▇▅▁▁▁ |
| diet_Vitamins_vit_b12 | 2 | 0 | 5.6e-01 | 0.00 | 5.6e-01 | 5.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_c | 1 | 0 | 9.7e-01 | 0.04 | 6.5e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_c | 2 | 0 | 9.3e-01 | 0.00 | 9.3e-01 | 9.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_beta_carotene | 1 | 0 | 2.1e-01 | 0.02 | 1.8e-01 | 2.4e-01 | ▅▁▁▇▁ |
| diet_Vitamins_beta_carotene | 2 | 0 | 1.8e-01 | 0.00 | 1.8e-01 | 1.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_lycopene | 1 | 0 | 4.0e-01 | 0.06 | 3.2e-01 | 6.5e-01 | ▅▇▁▁▁ |
| diet_Vitamins_lycopene | 2 | 0 | 3.2e-01 | 0.00 | 3.2e-01 | 3.2e-01 | ▁▁▇▁▁ |
view_tree(phylo_pruned) + ggtitle("Species-Level OTUs after Filtering")
Collapsing at genus level reduces complexity and allows genus‐scale ecological patterns to emerge with less interference from random error at the species-assignment level.
phylo_genus <- phylo_pruned %>% tax_glom("Genus")
skim_phyloseq(phylo_genus)
| Name | Piped data |
| Number of rows | 270270 |
| Number of columns | 86 |
| _______________________ | |
| Column type frequency: | |
| character | 8 |
| numeric | 77 |
| ________________________ | |
| Group variables | subject |
Variable type: character
| skim_variable | subject | n_missing | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| OTU | 1 | 0 | 6 | 11 | 0 | 702 | 0 |
| OTU | 2 | 0 | 6 | 11 | 0 | 702 | 0 |
| Sample | 1 | 0 | 6 | 8 | 0 | 166 | 0 |
| Sample | 2 | 0 | 8 | 10 | 0 | 219 | 0 |
| Kingdom | 1 | 0 | 11 | 11 | 0 | 1 | 0 |
| Kingdom | 2 | 0 | 11 | 11 | 0 | 1 | 0 |
| Phylum | 1 | 0 | 13 | 29 | 0 | 25 | 0 |
| Phylum | 2 | 0 | 13 | 29 | 0 | 25 | 0 |
| Class | 1 | 0 | 3 | 24 | 0 | 51 | 0 |
| Class | 2 | 0 | 3 | 24 | 0 | 51 | 0 |
| Order | 1 | 0 | 3 | 26 | 0 | 105 | 0 |
| Order | 2 | 0 | 3 | 26 | 0 | 105 | 0 |
| Family | 1 | 0 | 3 | 32 | 0 | 218 | 0 |
| Family | 2 | 0 | 3 | 32 | 0 | 218 | 0 |
| Genus | 1 | 0 | 3 | 26 | 0 | 699 | 0 |
| Genus | 2 | 0 | 3 | 26 | 0 | 699 | 0 |
Variable type: numeric
| skim_variable | subject | n_missing | mean | sd | p0 | p100 | hist |
|---|---|---|---|---|---|---|---|
| Abundance | 1 | 0 | 1.1e+01 | 135.14 | 0.0e+00 | 7.8e+03 | ▇▁▁▁▁ |
| Abundance | 2 | 0 | 9.1e+00 | 119.98 | 0.0e+00 | 9.2e+03 | ▇▁▁▁▁ |
| subject_sex | 1 | 0 | 2.0e+00 | 0.00 | 2.0e+00 | 2.0e+00 | ▁▁▇▁▁ |
| subject_sex | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| subject_day | 1 | 0 | 8.4e+01 | 47.92 | 1.0e+00 | 1.7e+02 | ▇▇▇▇▇ |
| subject_day | 2 | 0 | 2.8e+02 | 63.22 | 1.7e+02 | 3.8e+02 | ▇▇▇▇▇ |
| collection_day | 1 | 0 | 1.0e+02 | 62.09 | 1.0e+00 | 4.2e+02 | ▇▇▂▁▁ |
| collection_day | 2 | 0 | 1.6e+02 | 95.94 | 1.0e+00 | 3.3e+02 | ▇▇▇▆▇ |
| collection_date | 1 | 0 | 2.0e+04 | 62.09 | 2.0e+04 | 2.0e+04 | ▇▇▂▁▁ |
| collection_date | 2 | 0 | 2.0e+04 | 95.94 | 2.0e+04 | 2.0e+04 | ▇▇▇▆▇ |
| environment_holding | 1 | 0 | 1.6e+00 | 0.48 | 1.0e+00 | 2.0e+00 | ▅▁▁▁▇ |
| environment_holding | 2 | 0 | 1.4e+00 | 0.49 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▆ |
| environment_pair_access | 1 | 0 | 1.1e+00 | 0.29 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| environment_pair_access | 2 | 0 | 1.1e+00 | 0.22 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| repro_warb_status | 1 | 0 | 1.4e+00 | 0.73 | 1.0e+00 | 3.0e+00 | ▇▁▁▁▂ |
| repro_warb_status | 2 | 0 | 2.0e+00 | 0.96 | 1.0e+00 | 3.0e+00 | ▇▁▂▁▇ |
| bristol_min | 1 | 2808 | 3.1e+00 | 1.02 | 0.0e+00 | 6.0e+00 | ▁▂▇▁▂ |
| bristol_min | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_mean | 1 | 0 | 3.5e+00 | 1.17 | 0.0e+00 | 6.0e+00 | ▁▃▇▃▂ |
| bristol_mean | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_max | 1 | 2808 | 3.8e+00 | 1.55 | 0.0e+00 | 6.0e+00 | ▁▃▇▁▆ |
| bristol_max | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| supplement_probiotic | 1 | 0 | 7.1e-01 | 0.44 | 0.0e+00 | 1.0e+00 | ▃▁▁▁▇ |
| supplement_probiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_steroid | 1 | 0 | 7.0e-01 | 0.43 | 0.0e+00 | 1.0e+00 | ▃▁▂▁▇ |
| supplement_steroid | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antibiotic | 1 | 0 | 2.0e-02 | 0.13 | 0.0e+00 | 1.0e+00 | ▇▁▁▁▁ |
| supplement_antibiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_name | 1 | 0 | 1.7e+00 | 0.49 | 1.0e+00 | 3.0e+00 | ▅▁▇▁▁ |
| diet_name | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_total | 1 | 0 | 6.0e-01 | 0.04 | 5.4e-01 | 7.3e-01 | ▅▁▇▁▁ |
| diet_Total_total | 2 | 0 | 5.4e-01 | 0.00 | 5.4e-01 | 5.4e-01 | ▁▁▇▁▁ |
| diet_Protein_total | 1 | 0 | 6.7e-01 | 0.02 | 6.0e-01 | 6.9e-01 | ▁▁▁▇▅ |
| diet_Protein_total | 2 | 0 | 6.9e-01 | 0.00 | 6.9e-01 | 6.9e-01 | ▁▁▇▁▁ |
| diet_Fat_total | 1 | 0 | 6.2e-01 | 0.01 | 6.1e-01 | 7.0e-01 | ▇▅▁▁▁ |
| diet_Fat_total | 2 | 0 | 6.3e-01 | 0.00 | 6.3e-01 | 6.3e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_total | 1 | 0 | 3.4e-01 | 0.04 | 2.9e-01 | 6.0e-01 | ▅▇▁▁▁ |
| diet_CHO_by_diff_total | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Ash_total | 1 | 0 | 1.0e+00 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_total | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_dry_matter | 1 | 0 | 5.6e-01 | 0.01 | 5.3e-01 | 5.6e-01 | ▁▁▁▅▇ |
| diet_Total_dry_matter | 2 | 0 | 5.5e-01 | 0.00 | 5.5e-01 | 5.5e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 1 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Foods_biscuit_rotation | 1 | 0 | 2.3e-01 | 0.02 | 0.0e+00 | 2.5e-01 | ▁▁▁▁▇ |
| diet_Foods_biscuit_rotation | 2 | 0 | 2.5e-01 | 0.00 | 2.5e-01 | 2.5e-01 | ▁▁▇▁▁ |
| diet_Foods_invertebrate_misc | 1 | 0 | 1.5e-01 | 0.03 | 1.3e-01 | 2.6e-01 | ▇▁▅▁▁ |
| diet_Foods_invertebrate_misc | 2 | 0 | 1.9e-01 | 0.00 | 1.9e-01 | 1.9e-01 | ▁▁▇▁▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 1 | 0 | 2.1e-01 | 0.01 | 2.0e-01 | 2.4e-01 | ▇▁▁▅▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Foods_protein_rotation | 1 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 7.0e-02 | ▇▁▁▁▁ |
| diet_Foods_protein_rotation | 2 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 4.0e-02 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables | 1 | 0 | 3.2e-01 | 0.02 | 2.9e-01 | 4.3e-01 | ▅▇▁▁▁ |
| diet_Foods_seasonal_vegetables | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_ohdz_oatmeal_gel | 1 | 0 | 5.0e-02 | 0.04 | 0.0e+00 | 8.0e-02 | ▅▁▁▁▇ |
| diet_Foods_ohdz_oatmeal_gel | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Protein_taurine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Protein_taurine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Protein_methionine | 1 | 0 | 4.4e-01 | 0.01 | 3.2e-01 | 4.5e-01 | ▁▁▁▁▇ |
| diet_Protein_methionine | 2 | 0 | 4.5e-01 | 0.00 | 4.5e-01 | 4.5e-01 | ▁▁▇▁▁ |
| diet_Fat_omega_3_ala__epa__dha | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_3_ala__epa__dha | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Fat_omega_6_la__gla__aa | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_6_la__gla__aa | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_CHO_by_diff_starch | 1 | 0 | 9.5e-01 | 0.07 | 3.8e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_starch | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_ndf | 1 | 0 | 7.8e-01 | 0.01 | 7.5e-01 | 7.8e-01 | ▁▁▅▁▇ |
| diet_CHO_by_diff_ndf | 2 | 0 | 7.7e-01 | 0.00 | 7.7e-01 | 7.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_adf | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_adf | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_crude_fiber | 1 | 0 | 5.7e-01 | 0.01 | 5.7e-01 | 7.1e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_crude_fiber | 2 | 0 | 5.7e-01 | 0.00 | 5.7e-01 | 5.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_tdf | 1 | 0 | 4.1e-01 | 0.04 | 3.8e-01 | 7.6e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_tdf | 2 | 0 | 3.8e-01 | 0.00 | 3.8e-01 | 3.8e-01 | ▁▁▇▁▁ |
| diet_Ash_calcium | 1 | 0 | 9.6e-01 | 0.01 | 7.7e-01 | 9.7e-01 | ▁▁▁▁▇ |
| diet_Ash_calcium | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Ash_phosphorus | 1 | 0 | 9.6e-01 | 0.03 | 9.4e-01 | 1.0e+00 | ▇▁▁▁▅ |
| diet_Ash_phosphorus | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_potassium | 1 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 9.1e-01 | ▇▁▁▁▁ |
| diet_Ash_potassium | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_Ash_magnesium | 1 | 0 | 5.0e-01 | 0.05 | 4.4e-01 | 7.2e-01 | ▅▇▁▁▁ |
| diet_Ash_magnesium | 2 | 0 | 4.4e-01 | 0.00 | 4.4e-01 | 4.4e-01 | ▁▁▇▁▁ |
| diet_Ash_copper | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_copper | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iron | 1 | 0 | 9.8e-01 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iron | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_zinc | 1 | 0 | 9.8e-01 | 0.04 | 4.7e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_zinc | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_manganese | 1 | 0 | 9.9e-01 | 0.06 | 2.4e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_manganese | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iodine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iodine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_ca_p | 1 | 0 | 8.4e-01 | 0.02 | 6.9e-01 | 8.6e-01 | ▁▁▁▅▇ |
| diet_Ash_ca_p | 2 | 0 | 8.1e-01 | 0.00 | 8.1e-01 | 8.1e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_a_iu | 1 | 0 | 2.5e-01 | 0.02 | 2.3e-01 | 2.7e-01 | ▅▁▁▁▇ |
| diet_Vitamins_vit_a_iu | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_d3 | 1 | 0 | 9.8e-01 | 0.02 | 7.3e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_d3 | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_e | 1 | 0 | 9.3e-01 | 0.10 | 6.4e-01 | 1.0e+00 | ▁▁▅▁▇ |
| diet_Vitamins_vit_e | 2 | 0 | 8.0e-01 | 0.00 | 8.0e-01 | 8.0e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_k | 1 | 0 | 9.7e-01 | 0.04 | 4.0e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_k | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b1_thiamin | 1 | 0 | 9.8e-01 | 0.06 | 2.8e-01 | 9.9e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b1_thiamin | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b2_riboflavin | 1 | 0 | 9.0e-01 | 0.03 | 6.8e-01 | 9.4e-01 | ▁▁▁▇▅ |
| diet_Vitamins_vit_b2_riboflavin | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b3_niacin | 1 | 0 | 9.9e-01 | 0.04 | 4.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b3_niacin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_choline | 1 | 0 | 5.0e-01 | 0.01 | 4.6e-01 | 5.2e-01 | ▁▁▇▁▅ |
| diet_Vitamins_choline | 2 | 0 | 5.2e-01 | 0.00 | 5.2e-01 | 5.2e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b5_pantothenic_acid | 1 | 0 | 9.2e-01 | 0.04 | 3.9e-01 | 9.4e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b5_pantothenic_acid | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b6_pyridoxine | 1 | 0 | 9.6e-01 | 0.05 | 3.5e-01 | 9.6e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b6_pyridoxine | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b7_biotin | 1 | 0 | 9.9e-01 | 0.02 | 7.2e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b7_biotin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_folic_acid | 1 | 0 | 9.9e-01 | 0.07 | 5.0e-02 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_folic_acid | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b12 | 1 | 0 | 4.9e-01 | 0.07 | 4.5e-01 | 1.0e+00 | ▇▅▁▁▁ |
| diet_Vitamins_vit_b12 | 2 | 0 | 5.6e-01 | 0.00 | 5.6e-01 | 5.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_c | 1 | 0 | 9.7e-01 | 0.04 | 6.5e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_c | 2 | 0 | 9.3e-01 | 0.00 | 9.3e-01 | 9.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_beta_carotene | 1 | 0 | 2.1e-01 | 0.02 | 1.8e-01 | 2.4e-01 | ▅▁▁▇▁ |
| diet_Vitamins_beta_carotene | 2 | 0 | 1.8e-01 | 0.00 | 1.8e-01 | 1.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_lycopene | 1 | 0 | 4.0e-01 | 0.06 | 3.2e-01 | 6.5e-01 | ▅▇▁▁▁ |
| diet_Vitamins_lycopene | 2 | 0 | 3.2e-01 | 0.00 | 3.2e-01 | 3.2e-01 | ▁▁▇▁▁ |
view_tree(phylo_genus) + ggtitle("Genus-Level OTUs")
Let’s look at our OTUs now that we merged to the Genus level
rare_genera <- names(taxa_sums(phylo_genus)[taxa_sums(phylo_genus) <= 2])
keep_genera <- names(taxa_sums(phylo_genus)[taxa_sums(phylo_genus) > 2])
length(rare_genera)
[1] 89
length(keep_genera)
[1] 613
Let’s do one more pruning step to only keep the genera with total abundances greater than 2 (613 genera total).
phylo_clean <- prune_taxa(keep_genera, phylo_genus)
skim_phyloseq(phylo_clean)
| Name | Piped data |
| Number of rows | 236005 |
| Number of columns | 86 |
| _______________________ | |
| Column type frequency: | |
| character | 8 |
| numeric | 77 |
| ________________________ | |
| Group variables | subject |
Variable type: character
| skim_variable | subject | n_missing | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| OTU | 1 | 0 | 6 | 11 | 0 | 613 | 0 |
| OTU | 2 | 0 | 6 | 11 | 0 | 613 | 0 |
| Sample | 1 | 0 | 6 | 8 | 0 | 166 | 0 |
| Sample | 2 | 0 | 8 | 10 | 0 | 219 | 0 |
| Kingdom | 1 | 0 | 11 | 11 | 0 | 1 | 0 |
| Kingdom | 2 | 0 | 11 | 11 | 0 | 1 | 0 |
| Phylum | 1 | 0 | 13 | 29 | 0 | 23 | 0 |
| Phylum | 2 | 0 | 13 | 29 | 0 | 23 | 0 |
| Class | 1 | 0 | 3 | 24 | 0 | 50 | 0 |
| Class | 2 | 0 | 3 | 24 | 0 | 50 | 0 |
| Order | 1 | 0 | 3 | 26 | 0 | 98 | 0 |
| Order | 2 | 0 | 3 | 26 | 0 | 98 | 0 |
| Family | 1 | 0 | 3 | 32 | 0 | 198 | 0 |
| Family | 2 | 0 | 3 | 32 | 0 | 198 | 0 |
| Genus | 1 | 0 | 3 | 25 | 0 | 611 | 0 |
| Genus | 2 | 0 | 3 | 25 | 0 | 611 | 0 |
Variable type: numeric
| skim_variable | subject | n_missing | mean | sd | p0 | p100 | hist |
|---|---|---|---|---|---|---|---|
| Abundance | 1 | 0 | 1.2e+01 | 144.55 | 0.0e+00 | 7.8e+03 | ▇▁▁▁▁ |
| Abundance | 2 | 0 | 1.0e+01 | 128.35 | 0.0e+00 | 9.2e+03 | ▇▁▁▁▁ |
| subject_sex | 1 | 0 | 2.0e+00 | 0.00 | 2.0e+00 | 2.0e+00 | ▁▁▇▁▁ |
| subject_sex | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| subject_day | 1 | 0 | 8.4e+01 | 47.92 | 1.0e+00 | 1.7e+02 | ▇▇▇▇▇ |
| subject_day | 2 | 0 | 2.8e+02 | 63.22 | 1.7e+02 | 3.8e+02 | ▇▇▇▇▇ |
| collection_day | 1 | 0 | 1.0e+02 | 62.09 | 1.0e+00 | 4.2e+02 | ▇▇▂▁▁ |
| collection_day | 2 | 0 | 1.6e+02 | 95.94 | 1.0e+00 | 3.3e+02 | ▇▇▇▆▇ |
| collection_date | 1 | 0 | 2.0e+04 | 62.09 | 2.0e+04 | 2.0e+04 | ▇▇▂▁▁ |
| collection_date | 2 | 0 | 2.0e+04 | 95.94 | 2.0e+04 | 2.0e+04 | ▇▇▇▆▇ |
| environment_holding | 1 | 0 | 1.6e+00 | 0.48 | 1.0e+00 | 2.0e+00 | ▅▁▁▁▇ |
| environment_holding | 2 | 0 | 1.4e+00 | 0.49 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▆ |
| environment_pair_access | 1 | 0 | 1.1e+00 | 0.29 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| environment_pair_access | 2 | 0 | 1.1e+00 | 0.22 | 1.0e+00 | 2.0e+00 | ▇▁▁▁▁ |
| repro_warb_status | 1 | 0 | 1.4e+00 | 0.73 | 1.0e+00 | 3.0e+00 | ▇▁▁▁▂ |
| repro_warb_status | 2 | 0 | 2.0e+00 | 0.96 | 1.0e+00 | 3.0e+00 | ▇▁▂▁▇ |
| bristol_min | 1 | 2452 | 3.1e+00 | 1.02 | 0.0e+00 | 6.0e+00 | ▁▂▇▁▂ |
| bristol_min | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_mean | 1 | 0 | 3.5e+00 | 1.17 | 0.0e+00 | 6.0e+00 | ▁▃▇▃▂ |
| bristol_mean | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| bristol_max | 1 | 2452 | 3.8e+00 | 1.55 | 0.0e+00 | 6.0e+00 | ▁▃▇▁▆ |
| bristol_max | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| supplement_probiotic | 1 | 0 | 7.1e-01 | 0.44 | 0.0e+00 | 1.0e+00 | ▃▁▁▁▇ |
| supplement_probiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_steroid | 1 | 0 | 7.0e-01 | 0.43 | 0.0e+00 | 1.0e+00 | ▃▁▂▁▇ |
| supplement_steroid | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_fiber | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antibiotic | 1 | 0 | 2.0e-02 | 0.13 | 0.0e+00 | 1.0e+00 | ▇▁▁▁▁ |
| supplement_antibiotic | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| supplement_antidiarrheal | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_name | 1 | 0 | 1.7e+00 | 0.49 | 1.0e+00 | 3.0e+00 | ▅▁▇▁▁ |
| diet_name | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_total | 1 | 0 | 6.0e-01 | 0.04 | 5.4e-01 | 7.3e-01 | ▅▁▇▁▁ |
| diet_Total_total | 2 | 0 | 5.4e-01 | 0.00 | 5.4e-01 | 5.4e-01 | ▁▁▇▁▁ |
| diet_Protein_total | 1 | 0 | 6.7e-01 | 0.02 | 6.0e-01 | 6.9e-01 | ▁▁▁▇▅ |
| diet_Protein_total | 2 | 0 | 6.9e-01 | 0.00 | 6.9e-01 | 6.9e-01 | ▁▁▇▁▁ |
| diet_Fat_total | 1 | 0 | 6.2e-01 | 0.01 | 6.1e-01 | 7.0e-01 | ▇▅▁▁▁ |
| diet_Fat_total | 2 | 0 | 6.3e-01 | 0.00 | 6.3e-01 | 6.3e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_total | 1 | 0 | 3.4e-01 | 0.04 | 2.9e-01 | 6.0e-01 | ▅▇▁▁▁ |
| diet_CHO_by_diff_total | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Ash_total | 1 | 0 | 1.0e+00 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_total | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Total_dry_matter | 1 | 0 | 5.6e-01 | 0.01 | 5.3e-01 | 5.6e-01 | ▁▁▁▅▇ |
| diet_Total_dry_matter | 2 | 0 | 5.5e-01 | 0.00 | 5.5e-01 | 5.5e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 1 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Total_kcal | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Foods_biscuit_rotation | 1 | 0 | 2.3e-01 | 0.02 | 0.0e+00 | 2.5e-01 | ▁▁▁▁▇ |
| diet_Foods_biscuit_rotation | 2 | 0 | 2.5e-01 | 0.00 | 2.5e-01 | 2.5e-01 | ▁▁▇▁▁ |
| diet_Foods_invertebrate_misc | 1 | 0 | 1.5e-01 | 0.03 | 1.3e-01 | 2.6e-01 | ▇▁▅▁▁ |
| diet_Foods_invertebrate_misc | 2 | 0 | 1.9e-01 | 0.00 | 1.9e-01 | 1.9e-01 | ▁▁▇▁▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 1 | 0 | 2.1e-01 | 0.01 | 2.0e-01 | 2.4e-01 | ▇▁▁▅▁ |
| diet_Foods_mazuri_enrich_gum_arabic_5b35 | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Foods_protein_rotation | 1 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 7.0e-02 | ▇▁▁▁▁ |
| diet_Foods_protein_rotation | 2 | 0 | 4.0e-02 | 0.00 | 4.0e-02 | 4.0e-02 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables | 1 | 0 | 3.2e-01 | 0.02 | 2.9e-01 | 4.3e-01 | ▅▇▁▁▁ |
| diet_Foods_seasonal_vegetables | 2 | 0 | 2.9e-01 | 0.00 | 2.9e-01 | 2.9e-01 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_cooked_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_bean_green_fresh | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_carrot | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_pumpkin_canned | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_whole_raw_meat_prep | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_seasonal_vegetables_non_root | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_egg_white_only_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_potato_sweet_cooked | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_celery | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 1 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_lettuce_romaine | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Foods_ohdz_oatmeal_gel | 1 | 0 | 5.0e-02 | 0.04 | 0.0e+00 | 8.0e-02 | ▅▁▁▁▇ |
| diet_Foods_ohdz_oatmeal_gel | 2 | 0 | 0.0e+00 | 0.00 | 0.0e+00 | 0.0e+00 | ▁▁▇▁▁ |
| diet_Protein_taurine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Protein_taurine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Protein_methionine | 1 | 0 | 4.4e-01 | 0.01 | 3.2e-01 | 4.5e-01 | ▁▁▁▁▇ |
| diet_Protein_methionine | 2 | 0 | 4.5e-01 | 0.00 | 4.5e-01 | 4.5e-01 | ▁▁▇▁▁ |
| diet_Fat_omega_3_ala__epa__dha | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_3_ala__epa__dha | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Fat_omega_6_la__gla__aa | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Fat_omega_6_la__gla__aa | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_CHO_by_diff_starch | 1 | 0 | 9.5e-01 | 0.07 | 3.8e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_starch | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_ndf | 1 | 0 | 7.8e-01 | 0.01 | 7.5e-01 | 7.8e-01 | ▁▁▅▁▇ |
| diet_CHO_by_diff_ndf | 2 | 0 | 7.7e-01 | 0.00 | 7.7e-01 | 7.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_adf | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_CHO_by_diff_adf | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_crude_fiber | 1 | 0 | 5.7e-01 | 0.01 | 5.7e-01 | 7.1e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_crude_fiber | 2 | 0 | 5.7e-01 | 0.00 | 5.7e-01 | 5.7e-01 | ▁▁▇▁▁ |
| diet_CHO_by_diff_tdf | 1 | 0 | 4.1e-01 | 0.04 | 3.8e-01 | 7.6e-01 | ▇▁▁▁▁ |
| diet_CHO_by_diff_tdf | 2 | 0 | 3.8e-01 | 0.00 | 3.8e-01 | 3.8e-01 | ▁▁▇▁▁ |
| diet_Ash_calcium | 1 | 0 | 9.6e-01 | 0.01 | 7.7e-01 | 9.7e-01 | ▁▁▁▁▇ |
| diet_Ash_calcium | 2 | 0 | 9.7e-01 | 0.00 | 9.7e-01 | 9.7e-01 | ▁▁▇▁▁ |
| diet_Ash_phosphorus | 1 | 0 | 9.6e-01 | 0.03 | 9.4e-01 | 1.0e+00 | ▇▁▁▁▅ |
| diet_Ash_phosphorus | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_potassium | 1 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 9.1e-01 | ▇▁▁▁▁ |
| diet_Ash_potassium | 2 | 0 | 8.8e-01 | 0.00 | 8.8e-01 | 8.8e-01 | ▁▁▇▁▁ |
| diet_Ash_magnesium | 1 | 0 | 5.0e-01 | 0.05 | 4.4e-01 | 7.2e-01 | ▅▇▁▁▁ |
| diet_Ash_magnesium | 2 | 0 | 4.4e-01 | 0.00 | 4.4e-01 | 4.4e-01 | ▁▁▇▁▁ |
| diet_Ash_copper | 1 | 0 | 9.9e-01 | 0.05 | 3.1e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_copper | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iron | 1 | 0 | 9.8e-01 | 0.02 | 7.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iron | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_zinc | 1 | 0 | 9.8e-01 | 0.04 | 4.7e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_zinc | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_manganese | 1 | 0 | 9.9e-01 | 0.06 | 2.4e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_manganese | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_iodine | 1 | 0 | 9.9e-01 | 0.08 | 0.0e+00 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Ash_iodine | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Ash_ca_p | 1 | 0 | 8.4e-01 | 0.02 | 6.9e-01 | 8.6e-01 | ▁▁▁▅▇ |
| diet_Ash_ca_p | 2 | 0 | 8.1e-01 | 0.00 | 8.1e-01 | 8.1e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_a_iu | 1 | 0 | 2.5e-01 | 0.02 | 2.3e-01 | 2.7e-01 | ▅▁▁▁▇ |
| diet_Vitamins_vit_a_iu | 2 | 0 | 2.3e-01 | 0.00 | 2.3e-01 | 2.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_d3 | 1 | 0 | 9.8e-01 | 0.02 | 7.3e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_d3 | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_e | 1 | 0 | 9.3e-01 | 0.10 | 6.4e-01 | 1.0e+00 | ▁▁▅▁▇ |
| diet_Vitamins_vit_e | 2 | 0 | 8.0e-01 | 0.00 | 8.0e-01 | 8.0e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_k | 1 | 0 | 9.7e-01 | 0.04 | 4.0e-01 | 9.8e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_k | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b1_thiamin | 1 | 0 | 9.8e-01 | 0.06 | 2.8e-01 | 9.9e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b1_thiamin | 2 | 0 | 9.8e-01 | 0.00 | 9.8e-01 | 9.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b2_riboflavin | 1 | 0 | 9.0e-01 | 0.03 | 6.8e-01 | 9.4e-01 | ▁▁▁▇▅ |
| diet_Vitamins_vit_b2_riboflavin | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b3_niacin | 1 | 0 | 9.9e-01 | 0.04 | 4.9e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b3_niacin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_choline | 1 | 0 | 5.0e-01 | 0.01 | 4.6e-01 | 5.2e-01 | ▁▁▇▁▅ |
| diet_Vitamins_choline | 2 | 0 | 5.2e-01 | 0.00 | 5.2e-01 | 5.2e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b5_pantothenic_acid | 1 | 0 | 9.2e-01 | 0.04 | 3.9e-01 | 9.4e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b5_pantothenic_acid | 2 | 0 | 9.4e-01 | 0.00 | 9.4e-01 | 9.4e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b6_pyridoxine | 1 | 0 | 9.6e-01 | 0.05 | 3.5e-01 | 9.6e-01 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b6_pyridoxine | 2 | 0 | 9.6e-01 | 0.00 | 9.6e-01 | 9.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b7_biotin | 1 | 0 | 9.9e-01 | 0.02 | 7.2e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_b7_biotin | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_folic_acid | 1 | 0 | 9.9e-01 | 0.07 | 5.0e-02 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_folic_acid | 2 | 0 | 1.0e+00 | 0.00 | 1.0e+00 | 1.0e+00 | ▁▁▇▁▁ |
| diet_Vitamins_vit_b12 | 1 | 0 | 4.9e-01 | 0.07 | 4.5e-01 | 1.0e+00 | ▇▅▁▁▁ |
| diet_Vitamins_vit_b12 | 2 | 0 | 5.6e-01 | 0.00 | 5.6e-01 | 5.6e-01 | ▁▁▇▁▁ |
| diet_Vitamins_vit_c | 1 | 0 | 9.7e-01 | 0.04 | 6.5e-01 | 1.0e+00 | ▁▁▁▁▇ |
| diet_Vitamins_vit_c | 2 | 0 | 9.3e-01 | 0.00 | 9.3e-01 | 9.3e-01 | ▁▁▇▁▁ |
| diet_Vitamins_beta_carotene | 1 | 0 | 2.1e-01 | 0.02 | 1.8e-01 | 2.4e-01 | ▅▁▁▇▁ |
| diet_Vitamins_beta_carotene | 2 | 0 | 1.8e-01 | 0.00 | 1.8e-01 | 1.8e-01 | ▁▁▇▁▁ |
| diet_Vitamins_lycopene | 1 | 0 | 4.0e-01 | 0.06 | 3.2e-01 | 6.5e-01 | ▅▇▁▁▁ |
| diet_Vitamins_lycopene | 2 | 0 | 3.2e-01 | 0.00 | 3.2e-01 | 3.2e-01 | ▁▁▇▁▁ |
view_tree(phylo_clean) + ggtitle("Genus-Level OTUs")
Exporting intermediate objects saves time if you need to re‐run later steps without re‐processing.
phylo_melt_clean <- psmelt(phylo_clean)
clean_tree <- phy_tree(phylo_clean)
save(phylo_clean , file = "microeco/loris/phyloseq_genus.RData")
save(clean_tree , file = "microeco/loris/tree_genus.RData")
save(phylo_melt_clean, file = "microeco/loris/phyloseq_melt_genus.RData")
Working at multiple ranks lets you compare community structure from broad (Phylum) to fine (Genus) scales in the same pipeline.
fam_phylo <- phylo_clean %>% tax_glom("Family")
ord_phylo <- phylo_clean %>% tax_glom("Order")
cla_phylo <- phylo_clean %>% tax_glom("Class")
phy_phylo <- phylo_clean %>% tax_glom("Phylum")
view_tree(fam_phylo) + ggtitle("Family-Level OTUs")
view_tree(ord_phylo) + ggtitle("Order-Level OTUs")
view_tree(cla_phylo, "Class") + ggtitle("Class-Level OTUs") +
coord_cartesian(clip = "off") +
theme(plot.margin = margin(5, 65, 5, 5, "pt"))
view_tree(phy_phylo, "Phylum") + ggtitle("Phylum-Level OTUs") +
coord_cartesian(clip = "off") +
theme(plot.margin = margin(5, 65, 5, 5, "pt"))
fam_phylo_melt <- psmelt(fam_phylo)
ord_phylo_melt <- psmelt(ord_phylo)
cla_phylo_melt <- psmelt(cla_phylo)
phy_phylo_melt <- psmelt(phy_phylo)
fam_tree <- phy_tree(fam_phylo)
ord_tree <- phy_tree(ord_phylo)
cla_tree <- phy_tree(cla_phylo)
phy_tree <- phy_tree(phy_phylo)
save(fam_phylo , file = "microeco/loris/phyloseq_family.RData")
save(ord_phylo , file = "microeco/loris/phyloseq_order.RData")
save(cla_phylo , file = "microeco/loris/phyloseq_class.RData")
save(phy_phylo , file = "microeco/loris/phyloseq_phylum.RData")
save(fam_tree , file = "microeco/loris/tree_family.RData")
save(ord_tree , file = "microeco/loris/tree_order.RData")
save(cla_tree , file = "microeco/loris/tree_class.RData")
save(phy_tree , file = "microeco/loris/tree_phylum.RData")
save(fam_phylo_melt, file = "microeco/loris/phyloseq_melt_family.RData")
save(ord_phylo_melt, file = "microeco/loris/phyloseq_melt_order.RData")
save(cla_phylo_melt, file = "microeco/loris/phyloseq_melt_class.RData")
save(phy_phylo_melt, file = "microeco/loris/phyloseq_melt_phylum.RData")
In the microbiome_metrics
tutorial you will learn how to choose and apply rarefaction or
relative-abundance normalization, and then calculate fundamental
diversity statistics (α-diversity indices, β-diversity distances,
UniFrac, etc.). Refer to that section to decide when and how to rarefy
your merged tables, or to work directly on normalized counts for
non-phylogenetic metrics.